Pedobacter Explained

Pedobacter is a genus of Gram-negative soil-associated bacteria. Species including Pedobacter heparinus, formerly known as Flavobacterium heparinum, produce heparinase and are capable of using heparin as their sole carbon and nitrogen source.^[1]

In molecular biology, Pedobacter has also been identified as a contaminant of DNA extraction kit reagents and ultra-pure water systems, which may lead to its erroneous appearance in microbiota or metagenomic datasets.^[2]

Species

• Pedobacter africanus
• Pedobacter agri
• Pedobacter alluvionis
• Pedobacter arcticus
• Pedobacter borealis
• Pedobacter cryoconitis
• Pedobacter ginsengisoli
• Pedobacter heparinus
• Pedobacter insulae
• Pedobacter jejuensis
• Pedobacter lentus
• Pedobacter lusitanus^[3]
• Pedobacter nyackensis
• Pedobacter rhizosphaerae
• Pedobacter soli
• Pedobacter terricola

Further reading

• Kook. MooChang. Park. YongJin. Yi. Tae-Hoo. Pedobacter jejuensis sp nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter. International Journal of Systematic and Evolutionary Microbiology. 2014. 64. Part 5. 1789–1794. 10.1099/ijs.0.058024-0. 24573158. free.

Notes and References

1. Shaya. D. Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product. J. Biol. Chem.. 2006. 281. 22. 15525–35. 16565082. 10.1074/jbc.m512055200. free.
2. Salter. S. Cox. M. Turek. E. Calus. S. Cookson. W. Moffatt. M. Turner. P. Parkhill. J. Loman. N. Walker. A. Reagent contamination can critically impact sequence-based microbiome analyses. 2014. 10.1101/007187.
3. 10.1099/ijsem.0.001814. Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine. 2017. Covas. Cláudia. Caetano. Tânia. Cruz. Andreia. Santos. Tiago. Dias. Liliana. Klein. Guenter. Abdulmawjood. Amir. Rodríguez-Alcalá. Luis M.. Pimentel. Lígia L.. Gomes. Ana. Freitas. Ana Cristina. Garcia-Serrano. Alba. Fontecha. Javier. Mendo. Sónia. International Journal of Systematic and Evolutionary Microbiology. 67. 5. 1339–1348. 28109203. free.